DEgenes Hunter - CLUSTER 1 - Functional analysis report
Used data in this analysis
Specifically, in this experiment set, known experiment labels are:
- [Control] CTL_1
- [Control] CTL_2
- [Control] CTL_3
- [Control] CTL_4
- [Treatment] epm2a_1
- [Treatment] epm2a_2
- [Treatment] epm2a_3
- [Treatment] epm2b_1
- [Treatment] epm2b_2
- [Treatment] epm2b_3
- [Treatment] epm2b_4
General description
This report contains all the functional information that was requested by the options when functional_Hunter.R was executed. The functional categories can be:
- KEGG pathways
- GO:
- Biological Process
- Molecular Function
- Cellular Component
- Reactome pathways
- Custom nomenclature
All the functional categories are computed with CluterProfiler and GO caterogires are computed also with TopGo. Some sections will not show if there are not sinficative results. Each category is analysed using Over representation analysis (ORA) and Gene Set Analysis (GSEA). The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category. In the case of the GSEA method, all the genes are sorted by their fold-change and the algorithm scan which genes with similar fold-change shares a term of the selected functional category.
Statistics about input results obtained from DEGenes Expression Hunter are:
| Gene_tag | Genes |
|---|---|
| NOT_DEG | 843 |
| POSSIBLE_DEG | 10 |
| PREVALENT_DEG | 146 |
After apply a threshold of 0.05 over cluster correlation with Traits following relationships have been signifcant observed:
TEXTHERE: 
GO_MF enrichment results
GO_MF - Over Representation Analysis
The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.
Barplot
The plot shows the functional top significative terms in ascendant order by adjusted pvalue. The color represents the associated adjusted pvalue. The X axis represents the proportion of the known genes for a given functional term that are identified in the expression data.
Dotplot
The plot shows the top functional terms in descendant order by gene ratio. This ratio is the proportion of the known genes for a given functional term that are identified in the expression data. The color represents the associated adjusted pvalue. The X axis represents the gene ratio and the dot size the number of DEG genes associated to the functional term.
Gene-Concept Network
The network connects the top functional terms (brown nodes) to their associated genes (grey or colored nodes). The size of the functional terms shows the number of connected genes.
Cnetplot is not readable because more than 150 genes has been enriched in this nomenclature, so is not printed
Enrich Map plot
The network connects the top functional terms (nodes) between them trought their associates genes (grey edges, thickness represents the number of shared genes). The size of the functional terms shows the number of connected genes and the color the adjusted pvalue of the functional term.
Heatplot
Top functional terms are show in the Y axis whereas in the X axis are show the associated genes to them. The coloured squares indicates the fold change value.
Upsetplot
Top functional terms are listed the Y axis with the number of genes associated to them (Set size). Each column of dots marks one cluster of functional terms. The X axis indicates how many genes are shared exclusively for the members of one cluster.
Genes has been enriched in less than 2 categories, so Upsetplot cannot be printed
GO_BP enrichment results
GO_BP - Over Representation Analysis
The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.
Barplot
The plot shows the functional top significative terms in ascendant order by adjusted pvalue. The color represents the associated adjusted pvalue. The X axis represents the proportion of the known genes for a given functional term that are identified in the expression data.
Dotplot
The plot shows the top functional terms in descendant order by gene ratio. This ratio is the proportion of the known genes for a given functional term that are identified in the expression data. The color represents the associated adjusted pvalue. The X axis represents the gene ratio and the dot size the number of DEG genes associated to the functional term.
Gene-Concept Network
The network connects the top functional terms (brown nodes) to their associated genes (grey or colored nodes). The size of the functional terms shows the number of connected genes.
Cnetplot is not readable because more than 150 genes has been enriched in this nomenclature, so is not printed
Enrich Map plot
The network connects the top functional terms (nodes) between them trought their associates genes (grey edges, thickness represents the number of shared genes). The size of the functional terms shows the number of connected genes and the color the adjusted pvalue of the functional term.
Heatplot
Top functional terms are show in the Y axis whereas in the X axis are show the associated genes to them. The coloured squares indicates the fold change value.
Upsetplot
Top functional terms are listed the Y axis with the number of genes associated to them (Set size). Each column of dots marks one cluster of functional terms. The X axis indicates how many genes are shared exclusively for the members of one cluster.
Genes has been enriched in less than 2 categories, so Upsetplot cannot be printed
GO_CC enrichment results
GO_CC - Over Representation Analysis
The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.
Barplot
The plot shows the functional top significative terms in ascendant order by adjusted pvalue. The color represents the associated adjusted pvalue. The X axis represents the proportion of the known genes for a given functional term that are identified in the expression data.
Dotplot
The plot shows the top functional terms in descendant order by gene ratio. This ratio is the proportion of the known genes for a given functional term that are identified in the expression data. The color represents the associated adjusted pvalue. The X axis represents the gene ratio and the dot size the number of DEG genes associated to the functional term.
Gene-Concept Network
The network connects the top functional terms (brown nodes) to their associated genes (grey or colored nodes). The size of the functional terms shows the number of connected genes.
Cnetplot is not readable because more than 150 genes has been enriched in this nomenclature, so is not printed
Enrich Map plot
The network connects the top functional terms (nodes) between them trought their associates genes (grey edges, thickness represents the number of shared genes). The size of the functional terms shows the number of connected genes and the color the adjusted pvalue of the functional term.
Heatplot
Top functional terms are show in the Y axis whereas in the X axis are show the associated genes to them. The coloured squares indicates the fold change value.
Upsetplot
Top functional terms are listed the Y axis with the number of genes associated to them (Set size). Each column of dots marks one cluster of functional terms. The X axis indicates how many genes are shared exclusively for the members of one cluster.
Genes has been enriched in less than 2 categories, so Upsetplot cannot be printed
KEGG enrichment results
KEGG - Over Representation Analysis
The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.
Barplot
The plot shows the functional top significative terms in ascendant order by adjusted pvalue. The color represents the associated adjusted pvalue. The X axis represents the proportion of the known genes for a given functional term that are identified in the expression data.
Dotplot
The plot shows the top functional terms in descendant order by gene ratio. This ratio is the proportion of the known genes for a given functional term that are identified in the expression data. The color represents the associated adjusted pvalue. The X axis represents the gene ratio and the dot size the number of DEG genes associated to the functional term.
Gene-Concept Network
The network connects the top functional terms (brown nodes) to their associated genes (grey or colored nodes). The size of the functional terms shows the number of connected genes.
Cnetplot is not readable because more than 150 genes has been enriched in this nomenclature, so is not printed
Enrich Map plot
The network connects the top functional terms (nodes) between them trought their associates genes (grey edges, thickness represents the number of shared genes). The size of the functional terms shows the number of connected genes and the color the adjusted pvalue of the functional term.
Heatplot
Top functional terms are show in the Y axis whereas in the X axis are show the associated genes to them. The coloured squares indicates the fold change value.
Upsetplot
Top functional terms are listed the Y axis with the number of genes associated to them (Set size). Each column of dots marks one cluster of functional terms. The X axis indicates how many genes are shared exclusively for the members of one cluster.
Genes has been enriched in less than 2 categories, so Upsetplot cannot be printed
REACT enrichment results
REACT - Over Representation Analysis
The ORA method takes a group of significative DEGs (only DEGs, upregulated DEGs or downregulated DEGs) and performs a hypergeometric test for each term of the selected functional category.
Barplot
The plot shows the functional top significative terms in ascendant order by adjusted pvalue. The color represents the associated adjusted pvalue. The X axis represents the proportion of the known genes for a given functional term that are identified in the expression data.
Dotplot
The plot shows the top functional terms in descendant order by gene ratio. This ratio is the proportion of the known genes for a given functional term that are identified in the expression data. The color represents the associated adjusted pvalue. The X axis represents the gene ratio and the dot size the number of DEG genes associated to the functional term.
Gene-Concept Network
The network connects the top functional terms (brown nodes) to their associated genes (grey or colored nodes). The size of the functional terms shows the number of connected genes.
Cnetplot is not readable because more than 150 genes has been enriched in this nomenclature, so is not printed
Enrich Map plot
The network connects the top functional terms (nodes) between them trought their associates genes (grey edges, thickness represents the number of shared genes). The size of the functional terms shows the number of connected genes and the color the adjusted pvalue of the functional term.
Heatplot
Top functional terms are show in the Y axis whereas in the X axis are show the associated genes to them. The coloured squares indicates the fold change value.
Upsetplot
Top functional terms are listed the Y axis with the number of genes associated to them (Set size). Each column of dots marks one cluster of functional terms. The X axis indicates how many genes are shared exclusively for the members of one cluster.
Genes has been enriched in less than 2 categories, so Upsetplot cannot be printed